Interesting interview up at Gamasutra with one of the developers of the 3D Mario games, from Mario 64 to Mario Galaxy. They get into some pretty great detail:

One example [of a persistent problem with 3D] is the difficulty of stomping Goomba enemies in 3D, a basic, typical activity in a Mario game. “On the TV screen, objects don’t have the same kind of physicality,” [Koizumi] said. “That’s what makes it difficult to make people grasp the physicality and depth.”

One solution is adding shadow. “We decided to drop a shadow on the ground everywhere in Mario 64,” said Koizumi. “That way, every floating object would have a reference point on the ground.” Shadows are so effective at conveying depth, said Koizumi, that adding them has become an “iron-clad necessity,” having shadows fall directly under the character regardless of the light source. “It might not be realistic, but it’s much easier to play with the shadow directly below,” he added.

(Emphasis mine.) Or, how about this: Why is Mario Galaxy set on spherical planetoid levels?

Neither will the player get lost easily, or need to adjust the camera — by using spheres, Koizumi said, they had created a game field that never ended.